File Coverage

blib/lib/BioX/CLPM/Enzyme.pm

Criterion	Covered	Total	%
statement	3	3	100.0
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	4	4	100.0

package BioX::CLPM::Enzyme;
use base qw(BioX::CLPM::Base);
use Class::Std;
use Class::Std::Utils;

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('0.0.1');

{
        my %enzyme_id_of     :ATTR( :get      :set      :default<''>      :init_arg );
        my %name_of          :ATTR( :get           :set           :default<''>      :init_arg );
        my %clvg_sites_of    :ATTR( :get     :set     :default<''>      :init_arg );
        my %clvg_position_of :ATTR( :get  :set  :default<''>      :init_arg );
        my %rule_of          :ATTR( :get           :set           :default<''>      :init_arg );

        sub START {
                my ( $self, $ident, $arg_ref ) = @_;
                if ( $arg_ref ) { $self->_load( $arg_ref ); }
                return;
        }

        sub _load {
                my ( $self, $arg_ref ) = @_;
		# Update new enzyme_id if exists
                if ( defined $arg_ref->{enzyme_id} ) {
			my $enzyme_id = $arg_ref->{enzyme_id};
                	$self->set_enzyme_id($enzyme_id);

			# Load other enzyme data from db
	                my $sql  = 'select name, clvg_sites, clvg_position, rule ';
	                   $sql .= "from enzymes where enzyme_id = '$enzyme_id'";
	                my ( $enzyme_name, $clvg_sites, $clvg_position, $rule ) = $self->sqlexec( $sql, '@' );
			$self->set_name($enzyme_name);
			$self->set_clvg_sites($clvg_sites);
			$self->set_clvg_position($clvg_position);
			$self->set_rule($rule);
			warn "ENZYME _load() ( $enzyme_id, $enzyme_name, $clvg_sites, $clvg_position, $rule )\n";
		}
                elsif ( defined $arg_ref->{enzyme_name} ) {
			my $enzyme_name = $arg_ref->{enzyme_name};
                	$self->set_name($enzyme_name);

			# Load other enzyme data from db
	                my $sql  = 'select enzyme_id, clvg_sites, clvg_position, rule ';
	                   $sql .= "from enzymes where name = '$enzyme_name'";
	                my ( $enzyme_id, $clvg_sites, $clvg_position, $rule ) = $self->sqlexec( $sql, '@' );
                	$self->set_enzyme_id($enzyme_id);
			$self->set_clvg_sites($clvg_sites);
			$self->set_clvg_position($clvg_position);
			$self->set_rule($rule);
			warn "ENZYME _load() ( $enzyme_id, $enzyme_name, $clvg_sites, $clvg_position, $rule )\n";
		}
        }

	# API READ ONLY
	sub clvg_sites { my ( $self ) = @_; return split( //, $self->get_clvg_sites() ); }

	sub generate_fragments {
		my ($self, $arg_ref) = @_;
		my @clvg_sites;
		foreach my $sequence (@$arg_ref->{sequences}){
		        my @sequence = split(//, $sequence);
		        my $fragment;
		        my @initial_fragments;
		        foreach my $amino_acid (@sequence){
		                $fragment .= $amino_acid;
		                foreach my $clvg_site(@clvg_sites){
		                        if (uc($amino_acid) eq $clvg_site){
		                                push(@initial_fragments, $fragment);
		                                $fragment='';
		                        }
		                }
		        }
		        my @all_fragments = @initial_fragments;
		        for ( my $i = @initial_fragments - 1; $i > 1; $i--){
		                for ( my $j=0; $j<@initial_fragments-$i+1; $j++){
		                        my $new_fragment = '';
		                        $new_fragment.=$initial_fragments[$j];
		                        for ( my $k=0; $k<$i-1; $k++){
		                                $new_fragment.=$initial_fragments[$j+$k+1];
		                        }
		                        push (@all_fragments, $new_fragment);
		                }
		        }
		        foreach $fragment(@all_fragments){
		                if ($fragment=~m/.*[a-z]+.*/){
		                        #&SQLExec("insert into fragments(sequence_id, fragment_sequence) values ($sequence_id, '$fragment')");
		                }
		        }
		}
	}
}

1; # Magic true value required at end of module
__END__